Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray of laser capture microdissected Paneth cells from Atg16l1 T300A and wildtype littermates mice that were either exposed or not with mainstream cigarette smoking for 6 weeks

ABSTRACT: We found that mainstream cigarette smoking (4 cigarettes/day, 5 days/week for 2 weeks using Kentucky Research Cigarettes 3R4F) resulted in >20% decrease in the percentage of normal Paneth cell population in Atg16l1 T300A mice but showed minimal effect wildtype littermate control mice, indicating that Atg16l1 T300A polymorphism confers sensitivity to cigarette smoking-induced Paneth cell damage. We performed transcriptional profiling to identify molecular mechanisms associated with Paneth cell defect in Atg16l1 T300A mice exposed to cigarette smoking. Female mice were used at 4-5 weeks of age. Cigarette smoking was performed using smoking chamber with the dosage and schedule as described above. The Paneth cells of the mice were harvested by laser capture microdissection for transcriptomic analysis after completing 6 weeks of smoking.

ORGANISM(S): Mus musculus

SUBMITTER: Ta-Chiang Liu

PROVIDER: E-MTAB-6168 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

16S rRNA sequencing of fecal samples from Atg16l1 T300A and wildtype littermate mice that were either exposed or not to mainstream cigarette smoking for 6 weeks

2018-10-31 | E-MTAB-5717 | biostudies-arrayexpress

16S rRNA sequencing of fecal samples from Atg16l1 T300A and wildtype littermate mice that were exposed to mainstream cigarette smoking co-housed with mice from the same genotype but not exposed to cigarette smoking

Project description:We found that mainstream cigarette smoking (4 cigarettes/day, 5 days/week for 2 weeks using Kentucky Research Cigarettes 3R4F) resulted in >20% decrease in the percentage of normal Paneth cell population in Atg16l1 T300A mice but showed minimal effect in wildtype littermate control mice, indicating that Atg16l1 T300A polymorphism confers sensitivity to cigarette smoking-induced Paneth cell damage. We performed cohousing experiments to test if Paneth cell phenotype is horizontally transmissible as is microbiota. Atg16l1 T300A and littermate controls that were exposed to cigarette smoking were used as microbiota donors, and these donor mice were exposed to smoking for 2 weeks prior to cohousing. Separate groups of Atg16l1 T300A and littermate controls that were not exposed to cigarette smoking were used as microbiota recipients. The microbiota recipients were co-housed with microbiota donors of the same genotype for 4 weeks, during this period the donors continued to be exposed to cigarette smoking. Cigarette smoking was performed using smoking chamber with the dosage and schedule as described above. At the end of the experiment, the fecal microbiota composition was analyzed by 16S rRNA sequencing.

2018-10-31 | E-MTAB-5720 | biostudies-arrayexpress

RNA-seq of full thickness small intestine from Atg16l1 T300A and wildtype littermate mice that were either exposed or not with mainstream cigarette smoking for 6 weeks

Project description:We found that mainstream cigarette smoking (4 cigarettes/day, 5 days/week for 6 weeks using Kentucky Research Cigarettes 3R4F) resulted in >20% decrease in the percentage of normal Paneth cell population in Atg16l1 T300A mice but showed minimal effect in wildtype littermate control mice, indicating that Atg16l1 T300A polymorphism confers sensitivity to cigarette smoking-induced Paneth cell damage. We performed transcriptional profiling to identify molecular mechanisms associated with Paneth cell defect in Atg16l1 T300A mice exposed to cigarette smoking. Female mice were used at 4-5 weeks of age. Cigarette smoking was performed using smoking chamber with the dosage and schedule as described above. The whole ileum of the mice were harvested for transcriptomic analysis after completing 6 weeks of smoking.

2018-10-31 | E-MTAB-5707 | biostudies-arrayexpress

Comparison of the wild-type strain H99W with the hva1â, hva1â+HVA1 and a Galleria-passaged strain

Project description:Changes in gene expression of the serotype A wild-type strain H99W with the hva1â (8), hva1â+HVA1 (8-15) or a Galleria-passaged (P15) strain were examined during log-phase growth at 37 ÂºC. Analysis included two replicates of each comparison with a Cy3-Cy5 dye swap

2016-08-11 | E-GEOD-59582 | biostudies-arrayexpress

Transcription profiling of mouse intestinal epithelial spheroids cultured as stem cells, wound-associated epithelial cells or enterocytes

Project description:Intestinal epithelial spheroids were isolated from mouse jejunum as described in our previous publication (Miyoshi and Stappenbeck. In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture. Nature Protocols. 2013. PMID: 24232249) and then grown in 50% L-WRN conditioned medium (for stem cells) or differentiation medium containing dmPGE2 (for wound-associated epithelial cells) or differentiation medium containing EP4 inhibitor (for enterocytes). Transcription profiling was performed to gain insight into the characteristics distinguishing these cell types.

2016-10-25 | E-MTAB-3952 | biostudies-arrayexpress

Transcription profiling by array of mouse primary colonic stem cells, stem cells treated with butyrate, and differentiated colonocytes in vitro

Project description:Colonic epithelial stem cells were isolated from mouse colons as described in our previous publication (Miyoshi and Stappenbeck. In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture. Nature Protocols. 2013. PMID: 24232249) and then grown in 50% L-WRN conditioned medium (for stem cells) and treated with NaCl, 1mM or 10mM butyrate. Other samples of stem cells were treated with differentiation medium to produce colonocytes. Transcription profiling was performed to gain insight into the characteristics distinguishing these treatment and differentiation states.

2016-04-30 | E-MTAB-4005 | biostudies-arrayexpress

IL-17A treatment of mouse primary colonic epithelial spheroids in 3 differentiation states

Project description:The objective was to determine the transcriptional effect of IL-17A on primary colonic epithelial cells in various differentiation states in vitro. The three states included 1) stem/progenitor cell spheroids grown in 50% L-WRN media as described in our previous publication (PMID: 24232249), 2) differentiating colonic epithelial spheroids (DM) placed in differentiation media without L-WRN for 24 hours, 3) terminally differentiated colonocyte spheroids placed in differentiation media without L-WRN for 48 hours as described in our previous publication (PMID: 27264604). Each condition was cultured with or without 20ng/ml recombinant mouse IL-17A for the final 24 hours.

2018-04-10 | E-MTAB-6365 | biostudies-arrayexpress

Comparative Analysis of Gene Expression Profiles in Infective and Developing Larvae of Brugia malayi and Brugia pahangi

Project description:Comparative analysis of gene expression profiles provided novel insights into the genes that are transcriptionally active in infective and developing larvae of two closely related species. Species differences may indicate different metabolic adaptations that could affect host specificity, tissue tropism, and pathogenicity Two biological replicates of infective (L3) or developing larval RNA used for hybridization, in duplicate, to examine the gene expression changes in Brugia larvae Brugia malayi vector derived third stage larvae (Bm VL3); Brugia pahangi vector derived third stage larvae (Bp VL3); Brugia pahangi L3 cultured in vitro (Bp cL3); Brugia pahangi L3 derived from peritoneal cavity of infected gerbils (Bp ipL3); Brugia pahangi migrating L3 (Bp mL3) from infected gerbils

2015-04-28 | E-GEOD-68301 | biostudies-arrayexpress

Timecourse of mAbs 18B7 or MOPC-21 (control) binding to Cryptococcus neoformans serotype D strains JEC21 or 24067 (52D) after 1, 2 or 4 hours at 37 C.

Project description:Changes in gene expression of serotype D strains JEC21 or 24067 (52D) were examined after incubation with mAb 18B7 or the control MOPC-21 for 1, 2 or 4 hours at 37 C. Analysis used incubation with a non-binding IgG1 mAb as a control for incubation with a protective IgG1 mAb 18B7 at different timepoints.

2012-02-23 | E-GEOD-35241 | biostudies-arrayexpress

Identification and characterization of HVA1 (CNAG_02591) in Cryptococcus neoformans

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-08-11 | E-GEOD-59583 | biostudies-arrayexpress